Re: volume from VMD and NAMD different?

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Aug 05 2005 - 17:38:27 CDT

yes this is correct, however, I am in the NVE ensemble and therefore my
system should not change its volume.

Brian

On Fri, 5 Aug 2005, Jim Phillips wrote:

>
> First, you seem to be calculating the volume from minmax as
> volume = (maxx + minx) * (maxy + miny) * (maxz - minz)
>
> If you do it correctly, your system is increasing in volume, with a max of
> around 860000 after equilibration. NAMD gives the volume of the periodic
> cell, as specified in the config file cellBasisVector[123] or .xsc file.
> If the periodic cell is full, then hydrogens will be sticking out the
> ends, and minmax will measure a greater volume than the periodic cell.
>
> -Jim
>
>
> On Fri, 5 Aug 2005, Brian Bennion wrote:
>
> >
> >
> > Hello,
> >
> > I have been doing some checking and am a bit puzzled by significant
> > differences in volume/minmax values for my system as I prep it.
> >
> > Shown below is a list of the dimensions from VMD, while my NAMD logs show
> > a constant value of 923636.6390. As you can see there is a significant
> > difference between ^^^^^^^^^^^ and 964243.
> >
> > Any ideas?
> >
> > Brian
> >
> >
> > The first protein structure after solvation
> > vmd > measure center atomselect0
> > 56.7788696289 53.1865577698 28.926109314
> > vmd > measure minmax atomselect0
> > {9.60099983215 7.13899993896 -9.27499961853} {103.963996887 99.2289962769
> > 67.18699646}
> > 113.56499671915,106.36799621586,76.46199607853
> >
> >
> > The first protein minimization
> > vmd > measure center atomselect1
> > 56.7812080383 53.1876869202 28.9241199493
> > vmd > measure minmax atomselect1
> > {9.60099983215 7.13899993896 -9.27499961853} {103.963996887 99.2289962769
> > 67.18699646}
> > 113.56499671915,106.36799621586,76.46199607853 = 923636.53205419
> >
> >
> > The first water minimization
> > vmd > measure center atomselect2
> > 56.7821578979 53.1882400513 28.9262428284
> > vmd > measure minmax atomselect2
> > {7.91300010681 5.50600004196 -10.3170003891} {105.897003174 101.152999878
> > 68.3010025024}
> > 113.81000328081,106.65899991996,78.6180028915 = 954333.01948221
> >
> >
> > Combined system minimization
> > vmd > measure center atomselect3
> > 56.7821617126 53.1882591248 28.9262313843
> > measure minmax atomselect3
> > {7.38999986649 5.38500022888 -10.7279996872} {106.850997925 101.248001099
> > 68.4260025024}
> > 114.24099779149,106.63300132788,79.1540021896 = 964243.01025232
> >
> > System after first heating to 298K
> > vmd > measure center atomselect4
> > 56.7866363525 53.2055130005 28.868429184
> > vmd > measure minmax atomselect4
> > {3.93581748009 0.995232284069 -10.0360746384} {110.403068542 104.675170898
> > 67.9366989136}
> > 114.33888602209,105.67040318207,77.972773552 = 942085.46608153
> >
> >
> > ************************************************
> > Brian Bennion, Ph.D.
> > Bioscience Directorate
> > Lawrence Livermore National Laboratory
> > P.O. Box 808, L-448 bennion1_at_llnl.gov
> > 7000 East Avenue phone: (925) 422-5722
> > Livermore, CA 94550 fax: (925) 424-6605
> > ************************************************
> >
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:57 CST